248 lines
9.5 KiB
Java
248 lines
9.5 KiB
Java
package org.gcube.dataanalysis.geo.utils;
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import java.io.ByteArrayInputStream;
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import java.util.ArrayList;
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import java.util.Formatter;
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import java.util.LinkedHashMap;
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import java.util.List;
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import javax.xml.xpath.XPath;
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import javax.xml.xpath.XPathConstants;
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import javax.xml.xpath.XPathExpression;
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import javax.xml.xpath.XPathFactory;
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import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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import org.xml.sax.InputSource;
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import ucar.ma2.Array;
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import ucar.ma2.StructureData;
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import ucar.ma2.StructureMembers.Member;
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import ucar.nc2.constants.FeatureType;
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import ucar.nc2.dataset.CoordinateAxis;
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import ucar.nc2.dataset.CoordinateAxis1DTime;
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import ucar.nc2.dt.GridCoordSystem;
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import ucar.nc2.dt.GridDatatype;
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import ucar.nc2.dt.grid.GridDataset;
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import ucar.nc2.ft.FeatureCollection;
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import ucar.nc2.ft.FeatureDataset;
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import ucar.nc2.ft.FeatureDatasetFactoryManager;
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import ucar.nc2.ft.PointFeatureCollection;
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import ucar.nc2.ft.PointFeatureIterator;
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import ucar.nc2.ft.point.PointDatasetImpl;
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import ucar.nc2.ft.point.standard.StandardPointCollectionImpl;
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import ucar.unidata.geoloc.LatLonPointImpl;
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import ucar.unidata.geoloc.LatLonRect;
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public class ThreddsDataExplorer {
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// http://thredds.research-infrastructures.eu:8080/thredds/catalog/public/netcdf/catalog.xml
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public static String timePrefix = "time:";
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public static List<String> getFiles(String catalogURL) throws Exception {
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String xml = HttpRequest.sendGetRequest(catalogURL, null);
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XPath xpath = XPathFactory.newInstance().newXPath();
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XPathExpression xPathExpression = xpath.compile("//child::*[local-name()='catalog']/child::*[local-name()='dataset']/child::*[local-name()='dataset']");
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InputSource inputSource = new InputSource(new ByteArrayInputStream(xml.getBytes("UTF-8")));
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NodeList nodes = (NodeList) xPathExpression.evaluate(inputSource, XPathConstants.NODESET);
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List<String> fileNames = new ArrayList<String>();
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for (int i = 0; i < nodes.getLength(); i++) {
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Node node = nodes.item(i);
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String name = node.getAttributes().getNamedItem("name").getNodeValue();
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if (name != null)
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fileNames.add(name);
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}
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return fileNames;
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}
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public static LinkedHashMap<String, Double> retrieveDataFromNetCDF(String openDapLink, String layer, double x, double y) {
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try {
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LinkedHashMap<String, Double> map = new LinkedHashMap<String, Double>();
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if (isGridDataset(openDapLink)) {
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AnalysisLogger.getLogger().debug("Managing Grid File");
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return manageGridDataset(layer, openDapLink, x, y);
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}
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/*
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* else if (isPointDataset(openDapLink)) { AnalysisLogger.getLogger().debug("Managing Points File"); }
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*/
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else
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AnalysisLogger.getLogger().debug("Warning: the NETCDF file is of an unknown type");
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return map;
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("ERROR: " + e.getMessage());
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AnalysisLogger.getLogger().debug(e);
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e.printStackTrace();
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return null;
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}
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}
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// A GridDatatype is like a specialized Variable that explicitly handles X,Y,Z,T dimensions
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public static LinkedHashMap<String, Double> manageGridDataset(String layer, String filename, double x, double y) throws Exception {
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LinkedHashMap<String, Double> valuesMap = new LinkedHashMap<String, Double>();
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GridDataset gds = ucar.nc2.dt.grid.GridDataset.open(filename);
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List<GridDatatype> gridTypes = gds.getGrids();
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for (GridDatatype gdt : gridTypes) {
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AnalysisLogger.getLogger().debug("Inside File - layer name: "+gdt.getFullName());
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if (layer.equalsIgnoreCase(gdt.getFullName())) {
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AnalysisLogger.getLogger().debug("Found layer "+layer +" inside file");
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GridDatatype grid = gds.findGridDatatype(gdt.getName());
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GridCoordSystem gcs = grid.getCoordinateSystem();
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long timeSteps = 0;
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java.util.Date[] dates = null;
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if (gcs.hasTimeAxis1D()) {
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CoordinateAxis1DTime tAxis1D = gcs.getTimeAxis1D();
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dates = tAxis1D.getTimeDates();
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timeSteps = dates.length;
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} else if (gcs.hasTimeAxis()) {
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CoordinateAxis tAxis = gcs.getTimeAxis();
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timeSteps = tAxis.getSize();
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}
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int[] xy = gcs.findXYindexFromLatLon(y, x, null);
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for (int j = 0; j < timeSteps; j++) {
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Array data = grid.readDataSlice(j, 0, xy[1], xy[0]); // note order is t, z, y, x
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Double val = takeFirstDouble(data);
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if (!val.isNaN()) {
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String date = "" + j;
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if (dates != null)
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date = dates[j].toString();
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valuesMap.put(timePrefix + date, Double.parseDouble("" + val));
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}
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}
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break;
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}
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}
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return valuesMap;
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}
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public static Double takeFirstDouble(Array data) {
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long datal = data.getSize();
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Double val = Double.NaN;
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try {
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for (int k = 0; k < datal; k++) {
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Double testVal = data.getDouble(k);
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if (!testVal.isNaN()) {
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val = testVal;
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break;
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}
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}
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} catch (Exception ee) {
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> WARNING: Error in getting value: " + ee.getLocalizedMessage());
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}
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return val;
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}
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// A GridDatatype is like a specialized Variable that explicitly handles X,Y,Z,T dimensions
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public LinkedHashMap<String, String> managePointsDataset(String layer, String filename, double x, double y) throws Exception {
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LinkedHashMap<String, String> valuesMap = new LinkedHashMap<String, String>();
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float tolerance = 0.25f;
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Formatter errlog = new Formatter();
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FeatureDataset fdataset = FeatureDatasetFactoryManager.open(FeatureType.POINT, filename, null, errlog);
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PointDatasetImpl ds = (PointDatasetImpl) fdataset;
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List<FeatureCollection> lfc = ds.getPointFeatureCollectionList();
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for (FeatureCollection fc : lfc) {
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StandardPointCollectionImpl spf = (StandardPointCollectionImpl) fc;
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PointFeatureIterator iter = null;
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while ((y - tolerance > -90) && (x - tolerance > -180) && (y + tolerance < 90) && (x + tolerance < 180)) {
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LatLonRect rect = new LatLonRect(new LatLonPointImpl(y - tolerance, x - tolerance), new LatLonPointImpl(y + tolerance, x + tolerance));
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PointFeatureCollection coll = spf.subset(rect, null);
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iter = coll.getPointFeatureIterator(100 * 1000); // 100Kb buffer
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if (iter.getCount() == 0)
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iter.finish();
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else
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break;
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tolerance = tolerance + 0.25f;
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> tolerance = " + tolerance);
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}
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if (iter != null) {
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try {
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while (iter.hasNext()) {
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ucar.nc2.ft.PointFeature pf = iter.next();
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> EarthLoc: " + pf.getLocation());
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> EarthTime: " + pf.getObservationTime());
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StructureData sd = pf.getData();
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List<Member> mems = sd.getMembers();
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for (Member m : mems) {
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String unit = m.getUnitsString();
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if ((unit != null) && (unit.length() > 0)) {
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> description: " + m.getDescription());
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> data param: " + m.getDataParam());
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> name: " + m.getName());
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> unit: " + m.getUnitsString());
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> type: " + m.getDataType());
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Array arr = sd.getArray(m.getName());
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> is Time: " + m.getDataType());
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Double val = takeFirstDouble(arr);
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> extracted value: " + val);
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}
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}
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> EarthTime: ");
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}
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} finally {
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iter.finish();
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}
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}
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break;
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}
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return valuesMap;
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}
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// A GridDatatype is like a specialized Variable that explicitly handles X,Y,Z,T dimensions
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public static boolean isGridDataset(String filename) {
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try {
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Formatter errlog = new Formatter();
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FeatureDataset fdataset = FeatureDatasetFactoryManager.open(FeatureType.GRID, filename, null, errlog);
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if (fdataset == null) {
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// System.out.printf("GRID Parse failed --> %s\n", errlog);
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> NOT GRID");
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return false;
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} else
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return true;
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} catch (Exception e) {
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return false;
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}
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}
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// A GridDatatype is like a specialized Variable that explicitly handles X,Y,Z,T dimensions
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public static boolean isPointDataset(String filename) {
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try {
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Formatter errlog = new Formatter();
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FeatureDataset fdataset = FeatureDatasetFactoryManager.open(FeatureType.POINT, filename, null, errlog);
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if (fdataset == null) {
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> NOT POINT");
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return false;
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} else
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return true;
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} catch (Exception e) {
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return false;
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}
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}
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public static boolean isDataset(String filename) throws Exception {
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boolean isdataset = false;
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try {
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Formatter errlog = new Formatter();
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FeatureType[] fts = FeatureType.values();
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for (int i = 0; i < fts.length; i++) {
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FeatureDataset fdataset = FeatureDatasetFactoryManager.open(fts[i], filename, null, errlog);
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if (fdataset == null) {
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// System.out.printf(fts[i]+": Parse failed --> %s\n",errlog);
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} else {
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AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> " + fts[i] + " OK!");
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isdataset = true;
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}
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}
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} catch (Exception e) {
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}
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return isdataset;
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}
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}
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